Remote display issues¶
The GUI components in MRtrix3 (
shview) use the OpenGL
3.3 API to make full use of modern graphics cards. Unfortunately, X11
forwarding is not supported for OpenGL >= 3. There are a number of
reasons for this:
- OpenGL 1 & 2 used the OpenGL fixed function pipeline (now deprecated), whereas OpenGL >= 3 relies much more explicitly on shaders and buffer objects. Amongst other things, the use of buffer objects implies that potentially very large amounts of data be downloaded onto the GPU. In a X11 forwarding context, this would mean transferring these data over the network, which would probably end up being prohibitively slow in a sufficient number of situations that including support for it into the GLX was not thought to be worth the effort.
- X11 is unbelievably outdated, even according to the X.org developers themselves (as very clearly explained in this linux.conf.au talk). Current development efforts are going into its replacement, Wayland, which will start replacing X11 in earnest over the next few years (it’s already available and usable on the latest distributions). Thankfully, remote display capability is planned for Wayland, and support for it has already been added.
So it is not possible to use
shview over a standard
remote X11 connection.
Why does MRtrix3 use OpenGL 3.3 if it come with such limitations?¶
Because it’s clearly the most future-proof option. The older OpenGL versions are deprecated, and not recommended for modern applications. The OpenGL 3.3 API is much closer to the way modern graphics hardware works, and can therefore provide better performance. Finally, as explained above, X11 will eventually be phased out anyway...
What can be done about this?¶
There are a number of options available to deal with this, each with their own idiosyncraties. The simplest is to render locally (option 1), the other options require a fair bit of setting up on the server, and potentially also on the clients.
1. Use MRView locally¶
This is the simplest option, and allows the use of the local graphics hardware (much like X11 forwarding would have). To use this relatively seamlessly, the simplest option is to access the remote data using a network filesystem, such as SSHFS, SMB or NFS, and run MRView locally, loading the data from the network share. While this may seem inefficient, bear in mind that MRtrix3 will typically only load the data it needs to, so operation will probably not be slower than it would have been with the MRtrix 0.2.x version. Besides, the largest data files are likely to be track files (which will need to be loaded in their entirety); in the MRtrix 0.2.x version these needed to be streamed in whole over the network for every screen update.
Of the networked filesystems listed above, the simplest to use would probably be SSHFS, since it shouldn’t require any additional setup on the server (assuming users already have an SSH account), and is readily available on all platforms (using Win-SSHFS on Windows, OSXFuse on MacOSX).
2. Use an OpenGL-capable VNC server¶
Using the VNC protocol, the server is responsible for doing all the rendering remotely, and sends the resulting screen updates over the network. With this approach, users are presented with a full-blown desktop environment running on the server. This may consume too many resources on the remote server, depending on the desktop environment used. Also, since rendering is performed on the remote server, it needs to be equipped with an OpenGL 3.3 capable graphics stack - this means decent hardware and an up to date driver. However, it has the advantage of being widely supported and readily available on all platforms, with many implementations available. The only tricky part here is ensuring the VNC server is OpenGL-capable. As far as I can tell, x11vnc can be used for this.
3. Use VirtualGL to allow OpenGL forwarding within X11¶
The VirtualGL project offers a means of
rendering OpenGL graphics on the remote server, and sending the updated
contents of the OpenGL window to the local display, alongside the normal
X11 connection. This provides a means of running
mrview in a
potentially more familiar X11 over SSH session. As with the VNC
solution, rendering needs to be performed on the remote server, meaning
it needs to be equipped with an OpenGL 3.3 capable graphics stack - this
means decent hardware and an up to date driver. Also, it requires the
installation of additional software on the local system. Finally, for
this to work, all OpenGL commands need to be prefixed with
(not particularly problematic as this can be scripted or aliased). This
has been reported to work well with MRtrix3.
Unusual symbols on terminal¶
When running MRtrix commands on certain terminal emulators, you may see unusual characters appearing in the terminal output, that look something like the following:
$ mrinfo fa.mif -debug mrinfo: ←[00;32m[INFO] opening image "fa.mif"...←[0m mrinfo: ←[00;34m[DEBUG] reading key/value file "fa.mif"...←[0m mrinfo: ←[01;31m[ERROR] failed to open key/value file "fa.mif": No such file or directory←[0m
MRtrix uses VT100 terminal control codes to add colour to the terminal output, and to clear the terminal line of text when updating the text displayed during certain processes. Some terminal emulators may not have support for these codes, in which case unwanted characters and symbols may instead be displayed.
There are two possible solutions:
1. Use a different terminal emulator. In particular, earlier instructions for installing MRtrix3 on Windows involved the use of the terminal provided with Git for Windows; this is known to not support VT100 codes. The current recommendation for MRtrix3 Windows installation is based on MSYS2; the ‘MinGW-w64 Win64 Shell’ provided in this installation is known to support VT100 codes.
2. Terminal colouring can be disabled using the MRtrix configuration file <config>. Add the following line to either the system-wide or user config file to disable these advanced terminal features:
Processing of HCP data¶
We expect that a number of users will be wanting to use MRtrix3 for the analysis of data from the Human Connectome Project (HCP). These data do however present some interesting challenges from a processing perspective. Here I will try to list a few ideas, as well as issues that do not yet have a robust solution; I hope that any users out there with experience with these data will also be able to contribute with ideas or suggestions.
Do my tracking parameters need to be changed for HCP data?¶
Probably. For instance, the default parameters for length criteria are currently set based on the voxel size rather than absolute values (so e.g. animal data will still get sensible defaults). With such high resolution data, these may not be appropriate. The default maximum length is 100 times the voxel size, or only 125mm at 1.25mm isotropic; this would preclude reconstruction of a number of long-range pathways in the brain, so should be overridden with something more sensible. The minimum length is more difficult, but in the absence of a better argument I’d probably stick with the default (5 x voxel size, or 2 x voxel size if ACT is used).
Also, the default step size for iFOD2 is 0.5 times the voxel size; this will make the track files slightly larger than normal, and will also make the tracks slightly more jittery, but actually disperse slightly less over distance, than standard resolution data. People are free to experiment with the relevant tracking parameters, but we don’t yet have an answer for how these things should ideally behave.
Is it possible to use data from all shells in CSD?¶
Not yet. We are working on inclusion of Multi-Shell Multi-Tissue (MSMT) CSD into MRtrix3, and hopefully it will be there soon. For now, any command in MRtrix that operates on diffusion data will by default automatically select the largest b-value shell for processing.
The image data include information on gradient non-linearities. Can I make use of this?¶
Again, unfortunately not yet. Making CSD compatible with such data is more difficult than other diffusion models, due to the canonical response function assumption. To me, there are two possible ways that this could be handled:
- Use the acquired diffusion data to interpolate / extrapolate predicted data on a fixed b-value shell.
- Generate a representation of the response function that can be interpolated / extrapolated as a function of b-value, and therefore choose an appropriate response function per voxel.
Work is underway to solve these issues, but there’s nothing available yet. For those wanting to pursue their own solution, bear in mind that the gradient non-linearities will affect both the effective b-value and the effective diffusion sensitisation directions in each voxel. Otherwise, the FODs look entirely reasonable without these corrections...
The anatomical tissue segmentation for ACT from
act_anat_prepare_fsl seems even worse than for ‘normal’ data...?¶
The combination of high spatial resolution and high receiver coil density results in a pretty high noise level in the middle of the brain. This in turn can trick an intensity-based segmentation like FSL’s FAST into mislabeling things; it just doesn’t have the prior information necessary to disentangle what’s in there. I haven’t looked into this in great detail, but I would very much like to hear if users have discovered more optimal parameters for FAST, or alternative segmentation software, for which they have been impressed by the results.
Why does SIFT crash on my system even though it’s got heaps of RAM?¶
The main memory requirement for SIFT is that for every streamline, it must store a list of every fixel traversed, with an associated streamline length through each voxel. With a spatial resolution approximately double that of ‘standard’ DWI, the number of unique fixels traversed by each streamline will go up by a factor of around 3, with a corresponding increase in RAM usage. There is literally nothing I can do to reduce the RAM usage of SIFT; it’s fully optimised.
One thing you can do however, is just down-scale the FOD image prior to
mrresize in.mif out.mif -scale 0.5 -interp sinc. This
will reduce the RAM usage to more manageable levels, and realistically
probably won’t have that much influence on the algorithm anyway.
Importantly you can still use the high-resolution data for tracking (or
indeed anything else); it’s only the SIFT step that has the high RAM
usage. And using
mrresize rather than some other software to do the
downsampling will ensure that the down-sampled image is still properly
aligned with the high-resolution image in scanner space.
Generating Track-weighted Functional Connectivity (TW-FC) maps¶
This example demonstrates how these maps were derived, precisely as
performed in the relevant NeuroImage paper.
Assumes that you have a whole-brain tractogram named
a 3D volume named
FC_map.mif representing an extracted FC map with
Initial TWI generation:
tckmap tracks.tck temp.mif <-template / -vox options> -contrast scalar_map -image FC_map.mif -stat_vox mean -stat_tck sum
Deriving the mask (voxels with at least 5 streamlines with non-zero TW values):
tckmap tracks.tck - -template temp.mif -contrast scalar_map_count -image FC_map.mif | mrcalc - 5 -ge mask.mif -datatype bit
Apply the mask:
mrcalc temp.mif mask.mif -mult TWFC.mif